Mercurial > repos > iuc > bcftools_call
changeset 22:bf06b66ab5c2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 868f4386992de55d25da197660a43a913a09c8df
| author | iuc |
|---|---|
| date | Wed, 14 Aug 2024 16:43:44 +0000 |
| parents | 1001172b5089 |
| children | |
| files | bcftools_call.xml test-data/targets_file.tab |
| diffstat | 2 files changed, 34 insertions(+), 4 deletions(-) [+] |
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--- a/bcftools_call.xml Tue Jul 16 17:07:11 2024 +0000 +++ b/bcftools_call.xml Wed Aug 14 16:43:44 2024 +0000 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> <description>SNP/indel variant calling from VCF/BCF</description> <macros> <token name="@EXECUTABLE@">call</token> @@ -135,14 +135,19 @@ <option value="trio">trio - call genotypes given the father-mother-child constraint</option> </param> <when value="none"> - <expand macro="macro_restrict" type="target" label_type="Target" /> + <expand macro="macro_restrict" type="target" label_type="Target"> + <expand macro="macro_invert_targets"/> + </expand> </when> <when value="alleles"> <expand macro="macro_restrictions_file" type="target" label_type="Target" /> + <expand macro="macro_invert_targets"/> <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" /> </when> <when value="trio"> - <expand macro="macro_restrict" type="target" label_type="Target" /> + <expand macro="macro_restrict" type="target" label_type="Target"> + <expand macro="macro_invert_targets"/> + </expand> <expand macro="macro_novel_rate" /> </when> </conditional> @@ -171,7 +176,9 @@ <expand macro="macro_novel_rate" /> </when> </conditional> - <expand macro="macro_restrict" type="target" label_type="Target" /> + <expand macro="macro_restrict" type="target" label_type="Target"> + <expand macro="macro_invert_targets" type="target" label_type="Target" /> + </expand> <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)<FLOAT" /> </when> </conditional> @@ -312,6 +319,28 @@ </assert_contents> </output> </test> + <test> + <!-- Test targets-file option--> + <param name="input_file" ftype="vcf" value="mpileup.AD.vcf" /> + <param name="method" value="multiallelic" /> + <param name="output_type" value="v" /> + <section name="sec_consensus_variant_calling"> + <conditional name="variant_calling"> + <conditional name="genotypes"> + <conditional name="targets"> + <param name="targets_src" value="targets_file"/> + <param name="targets_file" value="targets_file.tab"/> + </conditional> + </conditional> + </conditional> + </section> + <output name="output_file"> + <assert_contents> + <has_text text="--targets-file" /> + <not_has_text text="DP=1;ADF=1;ADR=0;DPR=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=37" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ ==================================